Light is a fundamental environmental signal for living organisms. Photoreceptors convert light signals into biochemical and biological signals that ultimately regulate a wide range of important physiological processes such as photosynthesis, circadian rhythm and vision. Our long-term goal is to understand the signaling mechanisms of photoreceptors at the molecular level. We integrate crystallography, X-ray solution scattering, spectroscopic and biochemical approaches to investigate structures and signaling mechanisms of the red-/far-red-light photoreceptors, bacteriophytochromes (BphPs). BphPs absorb and respond to photons in the long wavelength range of the visible solar spectrum between 650nm and 900nm. A typical BphP photo-converts reversibly between red-light- absorbing (Pr) and far red-light-absorbing (Pfr) states, in which its C-terminal histidine kinase (HK) domain undergoes light-dependent auto-phosphorylation and then relays the phosphate group to a downstream response regulator in a two-component signaling pathway. At the center of this research are three core questions on signaling in BphPs. 1) What conformational changes are triggered in the chromophore upon absorbing a photon? 2) What is the nature of light-induced structural signals in the protein moiety? 3) How are local structural signals transmitted from the chromophore-binding site to the active site of the spatially distant HK? We address these questions by examining structures, dynamics and kinetic pathways of light-induced molecular events in three representative BphPs, on a wide range of time and length scales. We apply both static crystallography and mutagenesis to identify key structural elements and interactions in distinct signaling states. We conduct pump-probe experiments to initiate and follow photoreactions by X-ray scattering from both crystals and solutions of photoactive BphPs, to directly observe light-induced structural changes at room temperature. We thus explore the mechanism by which a red light signal is converted into a biological signal at the molecular level. In addition, the principles of long-range signal transduction in BphPs will have broader implications for understanding molecular mechanisms of more widespread, modular signaling proteins such as chemoreceptors. Since the range of the action spectrum of BphPs coincides with the therapeutic optical window for humans, BphPs have great potential as red fluorescent proteins for deep tissue fluorescent imaging and as genetically encoded tools for optical manipulation of in vivo functions. Our findings will serve as a structural framework to guide further development of BphP-based biomedical applications.